{"id":15037760,"url":"https://github.com/mdanalysis/mdanalysis","last_synced_at":"2025-05-12T20:48:36.026Z","repository":{"id":29844392,"uuid":"33389183","full_name":"MDAnalysis/mdanalysis","owner":"MDAnalysis","description":"MDAnalysis is a Python library to analyze molecular dynamics simulations.","archived":false,"fork":false,"pushed_at":"2025-04-18T18:35:26.000Z","size":534723,"stargazers_count":1416,"open_issues_count":495,"forks_count":709,"subscribers_count":41,"default_branch":"develop","last_synced_at":"2025-05-04T17:37:46.342Z","etag":null,"topics":["computational-chemistry","mdanalysis","molecular-dynamics","molecular-dynamics-simulation","molecular-simulation","python","science","trajectory-analysis"],"latest_commit_sha":null,"homepage":"https://mdanalysis.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MDAnalysis.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.bib","codeowners":null,"security":null,"support":null,"governance":"GOVERNANCE.md","roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2015-04-04T00:39:41.000Z","updated_at":"2025-05-03T09:22:37.000Z","dependencies_parsed_at":"2023-02-16T03:16:49.877Z","dependency_job_id":"5b21db0f-1cdc-4139-8658-2c24006fa292","html_url":"https://github.com/MDAnalysis/mdanalysis","commit_stats":{"total_commits":6107,"total_committers":263,"mean_commits":"23.220532319391634","dds":0.8215162927787785,"last_synced_commit":"e776f124c18c41f8990b487e8557d3ad82fe7d1f"},"previous_names":[],"tags_count":83,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fmdanalysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fmdanalysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fmdanalysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MDAnalysis%2Fmdanalysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MDAnalysis","download_url":"https://codeload.github.com/MDAnalysis/mdanalysis/tar.gz/refs/heads/develop","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253819949,"owners_count":21969445,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["computational-chemistry","mdanalysis","molecular-dynamics","molecular-dynamics-simulation","molecular-simulation","python","science","trajectory-analysis"],"created_at":"2024-09-24T20:35:34.404Z","updated_at":"2025-05-12T20:48:36.010Z","avatar_url":"https://github.com/MDAnalysis.png","language":"Python","readme":"================================\n  MDAnalysis Repository README\n================================\n\n|numfocus| \n\n|build| |cron| |cirruscron| |linters| |cov|\n\n|docs| |devdocs| |discussions|\n\n|pypi| |anaconda| |asv|\n\nMDAnalysis_ is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists. \n\nIt works with a wide range of popular simulation packages including GROMACS, Amber, NAMD, CHARMM, DL_POLY, HOOMD, LAMMPS and many others — see the lists of supported `trajectory formats`_ and `topology formats`_.\nMDAnalysis also includes widely used analysis algorithms in the `MDAnalysis.analysis`_ module.\n\n.. _numfocus-fiscal-sponsor-attribution:\n\nThe MDAnalysis project uses an `open governance model`_ and is fiscally sponsored by `NumFOCUS`_. Consider making \na `tax-deductible donation`_ to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.\n\n.. image:: https://www.mdanalysis.org/public/images/numfocus-sponsored-small.png\n   :alt: NumFOCUS (Fiscally Sponsored Project)\n   :target: https://numfocus.org/project/mdanalysis\n   :align: center\n\nThis project is bound by a `Code of Conduct`_.\n\n|powered_by_MDA|\n\nIf you use MDAnalysis_ in your project consider letting your users and the world know about it by displaying the MDAnalysis_ badge! `Embedding code`_ is available for different markups.\n\nExample analysis script\n=======================\n\n.. code:: python\n\n   import MDAnalysis as mda\n\n   # Load simulation results with a single line\n   u = mda.Universe('topol.tpr','traj.trr')\n\n   # Select atoms\n   ag = u.select_atoms('name OH')\n\n   # Atom data made available as Numpy arrays\n   ag.positions\n   ag.velocities\n   ag.forces\n\n   # Iterate through trajectories\n   for ts in u.trajectory:\n       print(ag.center_of_mass())\n\n\nDocumentation\n=============\n\n**New users** should read the `Quickstart Guide`_ and might want to\nlook at our videos_, in which core developers explain various aspects\nof MDAnalysis.\n\n**All users** should read the `User Guide`_.\n\n**Developers** may also want to refer to the `MDAnalysis API docs`_.\n\nA growing number of `tutorials`_ are available that explain how to\nconduct RMSD calculations, structural alignment, distance and contact\nanalysis, and many more.\n\n\nInstallation and availability\n=============================\n\nThe latest release can be **installed via pip or conda** as\ndescribed in the `Installation Quick Start`_.\n\n**Source code** is hosted in a git repository at\nhttps://github.com/MDAnalysis/mdanalysis and is packaged under the\nGNU Lesser General Public License, version 3 or any later version (LGPLv3+).\nIndividual source code components are provided under the\nGNU Lesser General Public License, version 2.1 or any later version (LGPLv2.1+).\nPlease see the file LICENSE_ for more information.\n\n\nContributing\n============\n\nPlease report **bugs** or **enhancement requests** through the `Issue\nTracker`_. Questions can also be asked on `GitHub Discussions`_.\n\nIf you are a **new developer** who would like to start contributing to\nMDAnalysis get in touch on `GitHub Discussions`_. To set up a\ndevelopment environment and run the test suite read the `developer\nguide`_.\n\n\nCitation\n========\n\nWhen using MDAnalysis in published work, please cite the following\ntwo papers:\n\n*   R\\. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,\n    M\\. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski,\n    S\\. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis:\n    A Python package for the rapid analysis of molecular\n    dynamics simulations. In S. Benthall and S. Rostrup,\n    editors, Proceedings of the 15th Python in Science\n    Conference, pages 102-109, Austin, TX, 2016. SciPy.\n    doi: `10.25080/Majora-629e541a-00e`_    \n*   N. Michaud-Agrawal, E. J. Denning, T. B. Woolf,\n    and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular\n    Dynamics Simulations. *J. Comput. Chem.* **32** (2011), 2319--2327.\n    doi: `10.1002/jcc.21787`_\n\nFor citations of included algorithms and sub-modules please see the references_.\n\n\n.. _NumFOCUS: https://numfocus.org/\n.. _open governance model: https://www.mdanalysis.org/about/#governance\n.. _tax-deductible donation: https://numfocus.org/donate-to-mdanalysis\n.. _`Code of Conduct`: https://www.mdanalysis.org/pages/conduct/\n.. _trajectory formats: https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1\n.. _topology formats: https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats\n.. _MDAnalysis: https://www.mdanalysis.org\n.. _LICENSE:\n   https://github.com/MDAnalysis/mdanalysis/blob/develop/LICENSE\n.. _`Installation Quick Start`:\n   https://www.mdanalysis.org/pages/installation_quick_start/\n.. _`MDAnalysis.analysis`: https://docs.mdanalysis.org/documentation_pages/analysis_modules.html\n.. _`tutorials`: https://userguide.mdanalysis.org/examples/README.html\n.. _`videos`: https://www.mdanalysis.org/pages/learning_MDAnalysis/#videos\n.. _`Quickstart Guide`:\n   https://userguide.mdanalysis.org/examples/quickstart.html\n.. _`User Guide`: https://userguide.mdanalysis.org\n.. _`MDAnalysis API docs`:\n   https://docs.mdanalysis.org\n.. _`Issue Tracker`: https://github.com/mdanalysis/mdanalysis/issues\n.. _`GitHub Discussions`:\n   https://github.com/MDAnalysis/mdanalysis/discussions\n.. _`developer guide`:\n   https://userguide.mdanalysis.org/contributing.html\n.. _`10.1002/jcc.21787`: https://dx.doi.org/10.1002/jcc.21787\n.. _`10.25080/Majora-629e541a-00e`: https://doi.org/10.25080/Majora-629e541a-00e\n.. _references: https://docs.mdanalysis.org/documentation_pages/references.html\n.. _Embedding code: https://www.mdanalysis.org/pages/citations/#powered-by-mdanalysis\n\n.. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg\n   :alt: Documentation (latest release)\n   :target: https://docs.mdanalysis.org\n\n.. |devdocs| image:: https://img.shields.io/badge/docs-development-yellow.svg\n   :alt: Documentation (development version)\n   :target: https://docs.mdanalysis.org/dev\n\n.. |numfocus| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat\u0026colorA=E1523D\u0026colorB=007D8A\n   :alt: Powered by NumFOCUS\n   :target: https://www.numfocus.org/\n\n.. |build| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml/badge.svg\n   :alt: Github Actions Build Status\n   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml\n\n.. |cron| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci-cron.yaml/badge.svg\n   :alt: Github Actions Cron Job Status\n   :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci-cron.yaml\n\n.. |cirruscron| image:: https://img.shields.io/cirrus/github/MDAnalysis/mdanalysis/develop\n   :alt: Cirrus CI - 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